Coexpression cluster:C1641

Full id: C1641_Mesenchymal_Nucleus_Fibroblast_tenocyte_Pericytes_normal_Smooth

Phase1 CAGE Peaks

Hg19::chr11:66103136..66103189,-	p2@RIN1
Hg19::chr7:100199967..100200012,+	p1@PCOLCE
Hg19::chr7:100200018..100200030,+	p2@PCOLCE
Hg19::chr7:100200840..100200890,+	p6@PCOLCE
Hg19::chr7:100201073..100201087,-	p2@ENST00000544873

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0005518	collagen binding	0.0324298847608999

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	2.14e-49	180
fibroblast	2.68e-26	75
contractile cell	6.75e-19	59
muscle precursor cell	1.03e-18	57
myoblast	1.03e-18	57
multi-potent skeletal muscle stem cell	1.03e-18	57
muscle cell	2.96e-18	54
electrically responsive cell	2.29e-17	60
electrically active cell	2.29e-17	60
smooth muscle cell	2.68e-13	42
smooth muscle myoblast	2.68e-13	42
skin fibroblast	1.55e-11	23
vascular associated smooth muscle cell	3.68e-09	32
stromal cell	1.07e-07	27

Uber Anatomy

Ontology term	p-value	n
somite	1.08e-25	83
paraxial mesoderm	1.08e-25	83
presomitic mesoderm	1.08e-25	83
presumptive segmental plate	1.08e-25	83
trunk paraxial mesoderm	1.08e-25	83
presumptive paraxial mesoderm	1.08e-25	83
dermomyotome	1.22e-22	70
organism subdivision	1.34e-19	365
skeletal muscle tissue	3.93e-19	61
striated muscle tissue	3.93e-19	61
myotome	3.93e-19	61
muscle tissue	4.21e-19	63
musculature	4.21e-19	63
musculature of body	4.21e-19	63
multilaminar epithelium	1.17e-18	82
trunk mesenchyme	2.80e-17	143
multi-cellular organism	2.81e-16	659
multi-tissue structure	5.03e-15	347
surface structure	1.64e-12	95
trunk	1.42e-11	216
anatomical system	4.61e-11	625
anatomical group	8.42e-11	626
integument	1.99e-10	45
integumental system	1.99e-10	45
cell layer	2.08e-10	312
tissue	6.44e-10	787
mesenchyme	6.60e-10	238
entire embryonic mesenchyme	6.60e-10	238
embryo	9.11e-10	612
epithelium	9.48e-10	309
unilaminar epithelium	9.82e-10	138
embryonic structure	5.23e-09	605
developing anatomical structure	5.23e-09	605
splanchnic layer of lateral plate mesoderm	7.56e-09	84
germ layer	8.87e-09	604
embryonic tissue	8.87e-09	604
presumptive structure	8.87e-09	604
epiblast (generic)	8.87e-09	604
skin of body	1.35e-08	40
vasculature	7.90e-07	79
vascular system	7.90e-07	79

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
RAD21#5885	3	6.2130203372738	0.00775105506881164	0.0318856325953844
REST#5978	3	5.79001722967681	0.00946878869443394	0.0356891559586411
TAL1#6886	2	11.9474466709761	0.010475778180992	0.0388012837338945

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.